Yes everything should play well together.
As to the sealed/flooded-if you have removable caps (or 2 that cover 3 cells each) you have flooded. If the caps are non removable, select sealed. If unsure look up the battery at store site to get correct type. Dont guess on this one-
The temp sensor on your controller is local to where its located-just ensure its not in direct path of AC or heat sun, probably in the designated cabinet will be fine. Some controllers have a remote sensor to measure ambient of actual battery location, yes it can make difference-optimally, but short of mounting in another outside location which I wouldn't -good to go. Was always going to get one as ours has allowance for remote temp sensor but never did-it works.
My opinion is if batteries are wired true parralel so should the controller be. + to one battery, - to the other. No reason not to, only cost some extra wire.
Have fun
